master guide v10 unpublished - daad

Biochemistry

Master of Science

v10 – 3 / 2017

Welcome

Welcome to the University of Tübingen and welcome to its biochemistry institute, the IFIB

(Interfaculty Institute of Biochemistry). Thank you for choosing this course and

congratulations on passing the competitive selection process.

You are now at the second stage of your university education. A period to discover and

develop your preferences in the field. And only one step away from your second major

professional decision after deciding what to study. At the end of the Master, you will choose

whether to continue along the academic track with a doctorate or whether to enter the job

market. We strive to support you, as best we can, with this decision.

You are also no longer a beginner in the field and we believe the structure of the master's

degree should strongly reflect this and support your further maturation towards becoming a

full-fledged biochemist. In our course, this shows in the small number of obligatory elements

and the large number of choices you can make. On the other hand, you have to invest more

time making decisions and organizing yourself. It also shows in that a significant part of the

degree will be dedicated to preparing you for future career decisions with seminars and

transferable skill courses.

We are looking forward to working with you and wish you all the best for the start of your

master's here in Tübingen.

Jakob Suckale, Coordinator

cover picture: albarst

Gerhard Groebe

Overview

The Tübingen Master of Biochemistry is a full-time 2-year program composed of 5 types of

elements (see table below). Students have to earn a minimum of 120 credit points in total,

each of which corresponds to approximately 30 hours of work including self study. All

4 elements are explained in detail later in the guide. Advanced Biochemistry and Current Topics are theoretical elements while modules, labs, and the master thesis are mixed

theoretical and practical elements.

Elements of the Master Credit points

Advanced Biochemistry 9

Current Topics 3

3 Modules 6+6+6

4 Labs 15+15+15+15

Master Thesis 30

120

The Tübingen Master of Biochemistry allows for a very flexible curriculum. You do not have

to take all the elements in a specific order or at a specific time. Nevertheless, we recommend

organizing your degree roughly according to the order above. The theoretical elements are a

good starting point to gain an overview of the moving field of biochemistry and are thus well

placed at the beginning. They may also serve as preparation for the laboratory work later on.

Modules are designed to be a transition from theory to more practical work, since they

contain both the background as well as the corresponding guided experiments. It also a good

way of getting to know your peers. Labs require more organization from your part and are

your stepping stone from predesigned modules to the more independent master thesis that

concludes the Master of Biochemistry.

A Master Plan

This page shows you one possible and

straightforward way to complete the Master of Biochemistry. Many variations on this theme

are possible and depend on your individual

preferences.

Year 1 - Intro, Modules, First Labs

The 1st year kicks off with a joint lectures series

by all the research group leaders of the

institute. Departing from the basics you have

acquired in your previous degree, this series

takes you into the advanced topics of

biochemistry and to the research frontier. In

parallel, you will choose your first modules and

your first lab placements.

In parallel to the lecture series, you will take a

course on current topics, which includes a

lecture series by guest speakers from outside

the institute and abroad presenting their latest

discoveries. In addition, you will most likely

select a 3rd

module and a 2nd

lab placement.

Year 2 - Modules, Labs & Master Project

As you enter the 2nd

year, the elements of the program will become longer and more in-depth

culminating in the master thesis at the end of the degree. You may decide to do one or more

of the research placements outside the institute or abroad. We will support you with national

and international placement using our contacts. At the end of the last semester, you will write

up the data collected during your thesis and present the results to the faculty.

During the entire degree you will be able to acquire transferable skills ranging from numerical

proficiency, IT, self-management and communication to interpersonal skills (purple track

above). The IFIB faculty will support you in your future professional decision following your

master in Tübingen and we hope that you will actively join our alumni network called Mobbel.

Variety

Here are a few ideas on how to adapt the template

presented on the previous page to your personal

preferences. Many variations are possible. Please

discuss them with us.

In case you want to delve deeper into a special topic or

in case you think one lab block is not enough to gain all

the experience you want, you can fuse 2 lab blocks into

1 continuous element accounting for 2x15 credits. Do

not chunk together more than 2 labs to make sure that

you also see a variety of research topics.

If you want to do one of your labs abroad, a double lab

may be useful. It takes time to organize a stint in

another country. To go through all this work for a single

lab element may not be efficient for you. Also, the

receiving group leader may be more willing to

accommodate you if you stay longer.

Another possibility to gain international experience is to

do your master thesis abroad. This element of the

master's degree is naturally longer, thus the ratio of

preparation and lab time is better than for a single lab.

On the other hand, it is an element that impacts on

your final grade, so you need to be more carefully to

select a good lab and a sure project.

In principle you can also take the Advanced Biochemistry lectures and the current topics during

different semesters. Keep in mind though that the

1st part of the transport lectures is conceptually

positioned before the 2nd

. The same goes for Current Topics. We recommend starting them early.

Advanced Biochemistry

The lecture series Advanced Biochemistry, nicknamed ABC, picks up where you left off with

the basic lecture series of the bachelor degree and takes you farther into the advanced

research topics. Reflecting this, the study material will be more papers and less textbooks,

and the hypotheses will be more controversial and less established.

The series consists of 2 parts: transport and signaling. The transport series has 2 parts (fall +

spring) while the signaling lectures are all in the spring semester.

Advanced Biochemistry is a relay of all the lecturers of the biochemistry institute. Every

lecturer has a block of consecutive presentations and then hands over to a colleague. This

will give you the chance to get to know the entire faculty of biochemistry and experience their

distinct research angles.

Element Overview

Goals Acquiring knowledge of the biochemistry governing cellular processes intra-

and intercellular communication

Content Extracellular matrix, cellular attachment, pathogen receptors, cellular uptake

processes, endocytosis, endosomal escape mechanisms, targeting/transport

in cells, organelle structure and maintenance, cytoskeleton, motor proteins,

signaling pathways, hormones

Format • Cellular transport processes (2 SWS in fall and 2 SWS in spring)

• Signal transduction (2 SWS in spring)

Duration 2 semesters in total (3x 1 semester series)

Recommended

semester

• Cellular transport processes: 1st + 2

nd semester

• Signal transduction (2 SWS in fall): 1st semester

Frequency Each lecture is offered once per year

Participants 6-30

Evaluation Oral examination with 2 professors or lecturers, at least one from the IFIB or

biochemistry section of the ZMBP about both lectures, 45 min/student

Responsible Dean of Studies in Biochemistry

Organizers Professors / lecturers of the IFIB and the ZMBP

Work load 90 h = 6 SWS

Credit points 9 CP

Transport - Advanced Biochemistry

The approximate overview of topics is

indicated in the table. Each lecturer is

responsible for their block of

presentations, typically taking place

every Tuesday morning.

The biochemical basics of cellular

transport processes will be reviewed

before proceeding to the topical

research questions and debates of the

field.

Unless you have started in spring, we

recommend to take the fall semester

lectures first, as it is partly the basis

for later lectures but the order can

also be reversed.

Details regarding the individual

lectures and teaching material will be

made available and updated on the

learning platform ILIAS.

Signaling - Advanced Biochemistry

In spring, in parallel to the 2nd

part of

the transport lectures, there is an

additional series on the biochemistry

of signaling processes.

In it you will get to know the remaining

group leaders of the IFIB plus

researchers from the next-door ZMBP,

specializing in plant biochemistry, one

of the strengths of Tübingen.

Signaling is a cutting edge field involved in most aspects of biochemistry. We chose the topic

partly because of the specialties of the in-house group leaders and because of its central

importance. Together with transport they both represent very active areas of biochemical

research. We hope you will enjoy our lectures and are looking forward to your feedback.

Examination

Advanced Biochemistry is one of the graded elements of the Master of Biochemistry. After

you have completed the series, there will be an approximately 45 minute oral examination by

2 lecturers on general biochemistry, the lecture series, and 2 external speakers of your

choosing.

See http://www.ifib.uni-tuebingen.de/master/examinations.html.

Current Topics in Biochemistry

Biochemistry is a fast moving field, which is why we want to dedicate an entire element of the

master's course to topical issues. Also, as master students you have already gained a lot of

experience, so we want to approach the material in a more collegial and dynamic format

rather than a typical frontal lecture.

Goals Extracting and discussing relevant information from a scientific presentation

Searching, interpreting and critically discussing published data

Presentation and discussion skills

Content Current findings, problems, and debates in biochemistry

Modern experimental approaches

Format Various interactive seminar formats, lectures by invited speakers

Duration The students have to attend the seminar series once during their curriculum.

The 20 lectures can be collected during the whole master program.

Recommended

semester

Seminar: 1st - 3

rd semester

Lectures: starting in the 1st semester

Frequency 10-12 invited speakers (typically Mondays) per term

Current topic seminars every fall term

Evaluation Invited speakers: attendance of 20 lectures (not graded)

Seminar: participation and attendance during 1 term (not graded)

Responsible Master coordinator

Work load Speakers: 22.5 h = 20 lectures = 1.5 SWS

Seminar: 30 h = 2 SWS

Credit points 3 CP

Modules

Modules are intended as both a transition from group practicals to independent research and

as a way to connect with your class mates and build your network. In contrast, during the

Labs you will rarely coincide with other master students. Modules last about a month and

consist of about 75h of work plus preparation time. They typically consist of a theoretical part

in the form of lectures and seminars and a practical part. Most are evaluated by a

combination of a protocol and an oral examination. You will select a total of at least

3 modules and receive 6 credit points for each successfully completed module.

IFIB Modules (at least 1 from this pool)

• Cell biochemistry of organelles (Rapaport & Dodt)

• Cell signaling (Feil)

• Chemical biology (Schwarzer)

• Disease mechanisms (Suckale)

• Genetic engineering (Gust, Fuß)

• In vivo crystallography (Duszenko)

• Membrane organization & dynamics (Garcia-Sáez)

• Molecular oncology (Schulze-Osthoff)

• Plant-pathogen interactions (Nürnberger & Felix)

• Innate immunity animals/plants (Nürnberger & Felix)

• Post-transcriptional control / RNA (Jansen)

• Structural biology (Stehle)

• Science of cooking (Garcia, Suckale)

Modules from Contributing Investigators

• Imaging from probe dev’t to in vivo application NEW

• Cell bio. w/ fluorescent fusion proteins (Rothbauer)

• Drug discovery technologies (Böckler, Exner)

• Immunology (Weber & colleagues)

• Microbial pathogens (Peschel, Götz & Wolz)

• Microscopy techniques (Liebig)

• Osteogenesis and wound closure (Ehnert, Nüssler)

• Pathobiochemistry (Weigert)

Apart from the requirement of at least 1 IFIB module, you are completely free to choose

according to your personal preferences and aims. You could, for example, focus on clinically

relevant topics like oncology, pharmacology and pathobiochemistry. Or you could hone your

technical skills with bioinformatics, microscopy, and toxicology techniques. It's up to you. You

can also take more than 3 modules if free places are available.

Timing of Modules

In designing the master degree we had to choose between unavoidable trade-offs. On the

one hand, a master with smoothly timed but compulsory elements. On the other hand, a

master that gives you choice but where timing problems may occur. We favor the latter since

it is important that you can develop your own personal profile and since we believe you are

capable of organizing yourself at the master stage.

The screenshots above are from the Master Calendar (http://tinyurl.com/mbioch-cal) or go to

the IFIB webpage under Master, subpage Links. Please refer to it when choosing your

modules. You can also subscribe to it depending on your local calendar software. Some

modules are offered both in fall and spring to allow you to minimize overlaps. Most of them

have no additional requirements and finish within a 4 week window. Please check the

module description below since a few modules deviate.

Let us know which modules you would like to have added and who may offer such a module.

We will try our best to convince the group leader(s) in question to invest the time to develop a

module.

A list of all the current modules follows below. Each module also has a page with details on

the learning platform ILIAS (https://ovidius.uni-tuebingen.de/ilias3/) which you can access

once formally signed up as a student.

IFIB Module - Cell Biochemistry of Organelles

Goals Experience in handling of cell cultures and yeast including principles of

subcellular fractionation of organelles; design and evaluation of experiments

for quantitative measurement of RNAi; experience in fluorescence microscopy

of mitochondria and peroxisomes; critical presentation and discussion of data

Content Topics: mitochondrial biogenesis and morphology;

peroxisome dynamics and function

Methods: subcellular fractionation, fluorescence microscopy, native gel

electrophoresis, transfection of cell cultures, RNAi, quantitative RT-PCR,

yeast genetics

Format Lecture (0.5 SWS), seminar (0.5 SWS), practical course (4 SWS)

Frequency Each spring term

Participants 4-12

Evaluation Audited protocol (not graded)

Oral presentation of the results and oral examination (=> grade)

Organizers Doron Rapaport, Gabriele Dodt

IFIB Module - Cell Biochemistry, Plant-Pathogen Interaction

Goals Introduction into independent lab work and planning of experiments, team

work (groups of 2), presentation of the experimental results in English

Content Introduction into modern molecular methods of cell biochemistry with the

model system of plant/pathogen interaction

Format Practical course + seminar (6 SWS)

Frequency Every term (e.g. Campus entry 2015 spring: http://bit.ly/1DNzomy)

Participants Up to 2

Evaluation Protocol (5-10 pages incl. introduction, methods, results & discussion) (50%)

Colloquium (50% of final grade)

Organizers Thorsten Nürnberger, Georg Felix, Birgit Kemmerling, Andrea Gust, Frederic

Brunner

IFIB Module - Cell Signaling

Goals Understanding of selected signal transduction modules that are important for

cardiovascular function in mammals

Evaluation of the relevance of biochemical research to improve our

understanding of human health and disease

Getting experience in handling and analysis of mammalian cells and stem

cells in particular

Design and performance of well-controlled experiments; documentation and

interpretation of data; critical presentation and discussion of data

Content Topics: signal transduction in mammalian cells, with a focus on the

cardiovascular system; visualization of signaling molecules in real time in

living cells; cell death and survival; transgenic mice as models for human

diseases; stem cell biology; regenerative medicine

Methods: biochemical analysis of signaling proteins; live cell imaging (e.g.

with FRET-based biosensors); analysis of gene expression (e.g.

immunohistochemistry on mouse tissue sections);cell growth assays;

generation of genetically-modified mice; Cre/lox recombination system;

culture of mammalian cells, in particular stem cell culture and differentiation;

iPS cell technology

Format Lecture/seminar (0.5 SWS), final seminar (0.5 SWS)

Practical course (4 SWS)


Participants 4-12

Evaluation Protocol (graded, 25%)

Performance at work (graded, 25%)

Oral examination (graded, 50%)

Organizers Robert Feil, Martin Thunemann, Susanne Feil

IFIB Module - Chemical Biology

Goals Exercise in advanced solid-phase peptide chemistry. Handling and synthesis

of building blocks for solid-phase peptide synthesis. Application of

chemoselective reactions for protein engineering. Development of strategies

for protein semisynthesis.

Content Topics: posttranslational modifications of proteins, chemical labeling of

proteins, protein chemistry

Methods: solid-phase peptide synthesis, organic chemistry, protein semi-

synthesis, methods for purification and analyses of semisynthetic proteins

Format Lecture (1 SWS), seminar (0.5 SWS), practical course (4 SWS)

Frequency Every term

Participants 2-6

Evaluation Protocol (10-15 pages including introduction, results and discussion) 50%

Oral examination (20 minutes) 50%

organizer Dirk Schwarzer

IFIB Module - Comparative Innate Immunity in Animals and Plants

Goals To get an overview on the state of research and current research topics of

plant molecular biology. To learn different presentation techniques to present

in English

Content Lecture concerning current topics of innate immunity in animals and plants.

The seminar consolidates the topics covered in the lecture by using original

publications.

Format Theory only: lecture (2 SWS, fall term) + seminar (1 SWS, spring term)

Frequency Each spring term (e.g. Campus entry spring '15: http://bit.ly/1EMSzRI)

Participants 4-30

Evaluation Oral examination (75%)

Oral presentation within the seminar (25%)

Organizers Thorsten Nürnberger, Georg Felix, Birgit Kemmerling, Andrea Gust, Frederic

Brunner

IFIB Module - Disease Mechanisms

Goals Gain a basic biochemical understanding of human disease processes

Summarize a disease mechanism with text and figures

Review a scientific text and suggest improvements

Discuss and debate a scientific topic

Content This course will explore the bewildering spectrum of molecular mechanisms

that lead to disease in humans. We will look at problems caused by other

species and by our own body, syndromes of dearth as well as plenty, damage

done by the chemical as well as the physical, and diseases of development

and degeneration.

While we cover these mechanisms you will gain a basic biochemical

understanding of the human body, its workings, and derailments. You will

learn why certain common diseases arise and you will discover that in many

cases it is far from clear why they do. You will see that diseases were in the

past named and grouped according to their symptoms, some times placing

diseases caused by very similar mechanisms confusingly far apart. You will

see that knowing the mechanism of a disease is the crucial piece of

information required before a treatment can be logically devised.

As part of the course you will prepare a review with text, figures, and citations

on a disease of your choosing. You will check somebody else's review and

you will take part in a debate.

Format Seminars/discussion (5 SWS) + practical (2 SWS) + lab seminar (1 SWS)


Participants 3-6

Evaluation Written review & peer review (1/3 of final grade)

Participation (1/3)

Oral examination (1/3)

Organizers Jakob Suckale

IFIB Module - Membrane Organization & Dynamics

Goals Understanding the principles of organization and dynamics of biological

membranes; role of biochemical and biophysical research, with a focus on

quantitative approaches, to improve our understanding of biological

membranes; experience in preparation, handling and analysis of membrane

model systems; design and performance of well-controlled experiments;

documentation and interpretation of data; critical presentation and discussion

of data

Content Topics: principles of lipid membrane assembly and structure; heterogeneity in

membrane composition and its relation to function; membrane fluidity;

membrane shape and its determinants; dynamic processes in membranes,

with a focus on shape changes, permeabilization, fusion and fission

Methods: preparation model membrane systems for microscopy experiments;

imaging of dynamic processes in membranes; analysis of membrane fluidity

and lateral organization; characterization of lipid phase diagrams; assays of

membrane permeabilization at the single vesicle level, including kinetics,

filling degree and pore size and stability; image processing and quantitative

data analysis

Format Seminar (0.5 SWS), final seminar (0.5 SWS), practical course (4 SWS)


Participants 4-8

Evaluation Protocol (graded, 25%)

Performance at work (graded, 10%)

Seminar presentation (graded, 25%)


Organizers Ana J. García-Sáez

IFIB Module - Modern Genetic Engineering

Goals Overview of the most important methods of modern genetic engineering and

their application in plants

Content Methods applied: PCR mutagenesis, Gateway cloning, DNA sequencing,

transient protein expression, transformation and PCR analysis, synthetic gene

design

Methods discussed: generation of genetically modified organisms, virus-

induced gene silencing, amiRNA technology, TALEN, lambda-red

Format Lectures (1 SWS), seminar (1 SWS), practical course (4 SWS)

Frequency Beginning of spring term

Participants 0-6 (together with 10 BSc students)

Evaluation Lab book (50% of final grade)

Presentation of results (50% of final grade)

Organizers Andrea Gust, Elisabeth Fuß

IFIB Module - Molecular Oncology

Goals Understanding of the major signaling pathways that promote carcinogenesis

and therapy resistance

Understanding of the major metabolic alterations in tumor cells

Understanding of the concept of cancer stem cells

Obtain insights in novel tumor therapies and conduct of clinical trials

Design and performance of well-controlled experiments; documentation and

interpretation of data; critical presentation and discussion of data

Content Topics: Principles of tumor biology; oncogenes and tumor suppressor genes;

cancer epigenetics; control of cell death and survival; apoptosis and

senescence; induced pluripotent and cancer stem cells, tumor metabolism;

translational oncology and personalized medicine; molecular targeted cancer

therapies, tumor immunotherapies.

Methods: biochemical analysis of signaling pathways; live cell imaging;

immunocytochemistry; kinase assays; immunoprecipitation; flow cytometry;

analysis of gene expression; assays for detection of apoptosis and

senescence, cell cycle analysis; culture of mammalian cells, in particular stem

cells; iPS cell technology

Format Seminar (0.5 SWS), final seminar (0.5 SWS), practical course (4 SWS),

lecture (2 SWS)

Frequency Labs each spring term, lecture series in fall

Participants 4-12

Evaluation Lab protocol (1/3 of final grade)

Performance at work (1/3 of final grade)

Lecture (Advanced Oncology) + written exam (1/3 of final grade)

Organizers Klaus Schulze-Osthoff, Frank Essmann

Note requires prior participation in the lecture and passing of the written exam

IFIB Module - Posttranscriptional Control of Gene Expression

Goals Experience in handling of RNA; design and evaluation of experiments for

quantitative measurement of RNA and proteins; design of control experiments

for quantitative measurements; critical presentation and discussion of data

Content Topics: mRNA stability; translation and its control; RNA-binding proteins

Methods: Northern blot; qRT-PCR; quantitative Western blot; RNP

purification; ribosome binding assays

Format Lecture (0.5 SWS), seminar (0.5 SWS), practical course (4 SWS)


Participants 4-8/12 (spring/fall)

Evaluation Audited protocol (not graded)

Oral presentation of the results (not graded)

Oral examination (=> grade)

organizer Ralf-Peter Jansen

IFIB Module - Structural Biology

Goals Understand the general flow of a structural analysis, practice of different

methods of crystallography (SIR, MAD, MR), identification of a protein by 3D-

NMR, set-up and analysis of NMR structure calculation, evaluation of

published data (significance, quality)

Content Topics: Practical aspects of structure determination using modern X-ray

crystallographic and NMR spectroscopic methods. Students will be trained to

solve structures and interpret their validity.

Methods: X-ray crystallography, NMR spectroscopy

Format Lecture/seminar (1 SWS), practical course (4 SWS)


Participants 4-8

Evaluation Oral examination (Þ grade)

Organizers Thilo Stehle, Remco Sprangers, Silke Wiesner

note Module requires the participation in a preparatory lecture series in fall

IFIB Module – Science of Cooking

Goals Understand the components of food and their positive and negative role. Why

is food prepared and how? Acquire a basic knowledge of food related

diseases. Quantitatively analyze the preparation of food and drink.

Content History of science and cooking, food components, basic transformation

processes during cooking: phase transitions, energy, temperature and heat

transfer; elasticity and texture; diffusion and spherification; viscosity and

polymers; emulsions and foams; baking and fermentation; applications in

haute cuisine and food industry.

Format Lectures (20h), Exercises (15h) and practical course (20h)

Frequency Every spring term

Participants 0-2 (together with up to 6 BSc students)

Evaluation Oral exam 60%

Protocol 20%

Project 15%

Active participation 5%

Organizers Ana J. García-Sáez, Jakob Suckale

External Module - Modulating osteogenesis and wound closure in vitro

Goals Experience in handling of cell cultures (isolation, expansion and differentiation

of primary human osteoblasts)

Design and evaluation of experiments for determining the effect of biological

substances/epigenetic drugs on osteoblast growth and function

Team work (groups of 2)

Presentation and discussion of the experimental results in English

Content Topic: Evaluating the effect of various biological substances/ epigenetic drugs

on osteoblast growth and function (osteogenesis)

Methods: Isolation and culture of primary human osteoblasts, viability tests,

proliferation measurement, enzyme activity measurement, histological

stainings (e.g. matrix mineralization), scratch assay for measuring wound

closure

Format Lecture/seminar (1 SWS), practical course (4 SWS)


Participants 4-8

Evaluation Written summary (2-5 pages) incl. materials, methods & results (30%)

Performance at work (30% of final grade)

Talk/poster presentation (40%)

Organizers Dr. Sabrina Ehnert, Prof. Andreas Nüssler

External Module - Cell Biochemistry with Fluorescent Fusion Proteins

Goals One of the major challenges in cell biology is to understand cellular processes

in response to external stimuli. The main goal is to localize cellular

components and understand their interactions. Fluorescent fusion proteins

are key factors to study the cellular distribution and dynamics of proteins in

living cells using time lapse analysis and High-Content Analysis based on

automated microscopy. To develop cellular models for compound or siRNA

screening, fluorescent fusion proteins have to be generated and expression of

fluorescent fusion proteins has to be validated in a number of disease

relevant cell lines.

Content In this course students will learn different aspects on how to generate

fluorescent fusion proteins in appropriate vector systems (PCR, cloning,

sequence analysis) as well as how to use them in various cellular and

biochemical assays (cell proliferation, immunoprecipitation, Western blotting).

You will learn cultivation of various human cell lines (sterile cell culture),

different techniques to transfect/transduce human cell lines with expression

vectors and how to analyze transfected cells on molecular and biochemical

level. Students will have access to various imaging techniques including live

cell analysis and immunofluorescence.

Format Practical course (5 SWS) seminar (0.5 SWS)

Frequency Each fall term

Participants 2-4

Evaluation Oral presentation at the start (1/3 of grade)

Audited protocol (1/3 of grade)

Oral examination (1/3 of grade)

Organizers Prof. Dr. Rothbauer

External Module - Drug Discovery Technologies

Goals Gaining basic knowledge and hands-on experience in the application of

(bio-)chemical, biophysical, and computational techniques for drug discovery.

Content Students typically select one of 3 fields of research: (a) chemical biology /

medicinal chemistry, (b) molecular biology & biophysics, (c) computational

biology & in silico drug discovery.

Tasks in these fields are: (a) synthesis and chemical characterization of tool

compounds for studying biological processes; assay design & development

utilizing such new compounds; studying structure-activity relationships in lead

development and optimization for elucidating key protein-ligand interactions

and their cooperativity; (b) construction and expression of vectors for protein

production; application of protein purification strategies; characterization of

protein-ligand interactions with biophysical techniques including NMR, ITC,

DSF, fluorescence polarization, etc.; implementation of compound screening

strategies and use of automation for improving throughput; (c) modeling

chemistry and biology at different levels of theory (QM, sQM, MM); studying

the dynamic behavior of proteins and protein-ligand interactions;

computational structure-based drug design; application of virtual screening

techniques including pharmacophores and (high-throughput) docking.

Format Seminar (0.5 SWS), practical course (7.5 SWS)

Frequency Once per year (seminar: during spring term; practical course: 3 weeks in

August – October by individual arrangement must be scheduled at the start of

each spring term)


Evaluation Audited protocol (~10 pages summary of research results + lab book) 50%

Oral presentation (~10 minutes) 50%

Organizers Frank Böckler, Thomas Exner

External Module – Imaging from probe development to in vivo application NEW

Goals Participants will gain a solid theoretical and practical foundation in clinically

relevant imaging techniques like positron emission tomography, magnetic

resonance, and computer tomography.

Content The module deals with the radiochemistry of imaging probes and with their

in vivo imaging. Participants will synthesize precursors for radiolabeling, learn

how to radiolabel, and finally apply these imaging probes in small live

laboratory animals. The module also involves detailed data analysis.

Synthesis of precursors, radiolabeling of precursors, PET, MR, SPECT, CT

and optical imaging, detailed data analysis of acquired data

Format Lectures (15h), practical lab work (40h), data analysis in seminars (4h),

literature seminar (4h)

Frequency Yearly

Participants 4-8

Evaluation Practical evaluation, exam, literature seminar evaluation

Organizers Florian Maier, Andreas Maurer

External Module - Immunology

Goals Skills: practical skills (experimental planning and execution, data analysis,

discussion), presentation, scientific writing

Knowledge: theory of immunological methods, insights into aspects of innate

and adaptive immunology

Content Students will be acquainted with the theoretical background for the following

immunology-related techniques in the introductory lecture block:

- Characteristics of the main innate and adaptive immune cells

- Working with blood- and skin-derived immune cells

- Isolation and phenotyping of cell types

- T-cell based assays and immune monitoring

- Immunohistochemistry / Immunofluorescence / Immunoblot / ELISA

- Flow cytometry (intracellular and surface stain; phospho-flow cytometry)

- Immunological techniques in mice / immunological mouse models

In the following 3.5 weeks, 1-2 students will be assigned to the following

participating labs offering insights into their ongoing research and allowing

first-hand practical experience. Preferences will be considered if possible.

- T-cell assays and immune monitoring (C. Gouttefangeas, Immunology)

- Peptide vaccination: from discovery to drugs (S. Stevanovic, Immunology)

- Immune responses in the skin towards infection (B. Schittek, Dermatology)

- Immune responses in the context of cancer (H. Braumüller, Dermatology)

- Innate Immunity (A. Weber, Immunology)

- Dendritic cell immunity (S. Autenrieth, Internal Medicine)

Upon completion of the practical period, students will be requested to:

- present their lab project in a short Powerpoint presentation held during a

1-day colloquium in the final week (all students and PIs participate)

- generate a report detailing their research topic, data and discussion.

Format Lectures (1 SWS), practical (8 SWS), colloquium (0.5 SWS)


Participants 6-11

Evaluation Students present their lab project in a short Powerpoint presentation held

during a 1-day colloquium in the final week (all students and lab supervisors

participate) - 50% of the final grade

Participants also generate a protocol/report detailing their research topic, data

and discussion - 50% of the final grade

Organizer Alexander Weber

Requirements Attendance of the Immunology lectures at the Department is recommended

prior to completion of the module but not formally required. Students with prior

knowledge or experience in immunology gained in Tübingen or elsewhere

may be given preference should the module be oversubscribed.

External Module - Pathobiochemistry

Goals Experience in detection of phosphorylated proteins, design and evaluation of

experiments for detection of activated signal transduction, understanding and

interpretation of pathobiochemical alterations and disease-related biomarkers

in body fluids, critical presentation and discussion of data, presentation and

discussion of scientific publications

Content Topics: molecular mechanisms of metabolic regulation in health and disease,

insulin resistance and diabetic late complications, diagnostic tools for

detection of pathobiochemical alterations and disease-related biomarkers in

body fluids

Methods: cell culture, transfection of cells, immunodetection of

phosphorylated proteins, immunoprecipitation, point of care testing

Format lectures (2 SWS), seminar (0.5 SWS), practical course (2.5 SWS)


Participants 4-8

Evaluation Protocol (not graded)

Presentation of a recent scientific paper (graded, 30%)


Organizers Cora Weigert, Rainer Lehmann, Andreas Peter, Erwin Schleicher, Harald

Staiger, Susanne Ullrich

External Module - Mechanisms of Microbial Pathogenicity

Goals Knowledge of molecular and cellular mechanisms of microbial pathogenicity

Content Theory taught in lectures

- How do bacteria survive in humans and cause infections?

- How does our defense work and how is it circumvented by bacteria?

- Which are the most topical and most urgent infectious diseases?

Practical course

- Salmonella mutagenesis

- Functional analysis of the type 3 secretion system

- Cell culture infection models of Salmonella

- Blue native gel electrophoresis

Format Lectures (fall term every Friday 8-10 AM, 2 SWS)

Seminar (Jan/Feb Monday 16:30)

Practical (2-week block end of spring term)

Frequency Once per year (fall + spring)


Evaluation Exam following the lecture (1/3)

Seminar grade (1/3)

Presentation following the practical (1/3)

Organizers Prof. Christiane Wolz, Prof. Samuel Wagner, Dr. Weidenmaier, Dr. Jürgens,

Dr. E. Bohn, Prof. Andreas Peschel, Prof. Fritz Götz

note See also W-Schiene: Mechanismen der Pathogenität von Mikroorganismen (4050), e.g. http://bit.ly/1bLV0ru. As this module is currently being rearranged,

the details are still in flux. Please confirm with the organizers before the start.

External Module - Microscopic Imaging Techniques

Goals Selection of an appropriate imaging technique and reliability to use it

Evaluation of quality and validity of published data

Content Detailed theoretical and practical knowledge of microscopic techniques (wide

field, fluorescence, life cell, confocal and electron microscopy)

Sample preparation, selection of the conditions to get and process an image

are taught and trained as well

The seminar gives an insight into newly developed imaging techniques.

Format Lecture/seminar (1.3 SWS), practical course (4.7 SWS)


Participants 4-8

Evaluation Written examination

Organizers Christian Liebig, Matthias Flötenmeyer, Gaspar Jekeley, Andrew Renault,

Frank Schleifenbaum, York Stierhof

Labs

Labs are mini research projects in biochemistry. They will consist of about 2 months of lab

work followed by a writing up or a final presentation depending on the group leader. You will

arrange your own labs by contacting selected principal investigators. All investigators of the

IFIB and external modules organizers automatically belong to this group. For all other labs

please contact us first by filling in the lab form.

We are thinking of labs as a way for you to test yourself

in different research areas of biochemistry. This will help

you determine which specialty is most suited to your

preferences and skills in a relatively short amount of time.

After having explored different corners of biochemistry

you will be in a better position to decide where to do a

doctorate or in which area of industry to seek

employment. For the same reason don't do more than

2 labs with the same group.

Labs often cannot be graded reliably because the results

depend not only on your skills and work ethics but also

on luck in the lab. Also, labs done abroad may shorten

your effective working time at the bench and thus

decrease your data output. This is why we have decided

not to ask for these elements of the Master of Biochemistry to be graded. We believe this will give you

more liberties to test with topics of modern biochemical

research interest you.

In total, you will select 4 labs, one of which has to be in

the IFIB. With 4x 15 CPs, or 60 points in total, the labs

will be the largest part of your master. You can do 1 or

more labs in other German laboratories or even abroad.

If you want to spend more time on a topic, you can fuse

to labs into one for a total of about 4 months.

When looking for a lab, keep in mind that at your stage

you require good supervision to learn effectively. This

can be harder to find in large, occasionally more

impersonal groups. We are collecting your feedback on labs to build a database to help you

profit from previous students' experience when looking for labs. This can be especially

important for industry labs who are often inaccessible without personal contacts.

Goals Study of published data in preparation for experimental work

Practicing the flow from hypothesis via experimental design and controls to

analysis of the results and interpretation within the context of current data

Documentation, oral and written presentation of data

Duration 8 weeks

Evaluation Audited protocol and oral presentation of the results and/or the theoretical

background (all not graded)

Responsible MSc biochemistry coordinator

Organizers IFIB group leaders, module organizers, other labs after confirmation

Credit points 15 CP

Master Thesis

Your master thesis concludes the 2-year degree

program with us. After having brushed up on the

theoretical underpinnings in the lecture and

Current Topic series, after having done more

organized practicals in several modules and

then in more self-organized laboratory

placements, the master thesis will be your most

independent and in-depth piece of research to

date.

This is reflected in its setup. The longer time

allotted, gives you more time to dig deeper into

the topic of your choice. More than in the labs

before, we expect you to actively develop your

research plan before conducting experiments.

The write up will also be more extensive and

evaluated more thoroughly.

After doing several labs, you will have gained a good overview of several biochemical

research areas. Carefully choose which thesis topic is most suited as it will influence future

choices regarding a doctorate or your job search. The topic of the master thesis has to be

clearly separate from any previous projects in the same lab, if any.

As with the labs, the master thesis can also be done abroad if you wish. As it needs to be

formally graded and influences your final master grade, please consult us during your

decision process. You will also need a 2nd

supervisor in the IFIB.

We hope that the master thesis will bring you a step closer to becoming an independent and

fully fledged biochemical researcher.

Goals Survey published data to develop a novel hypothesis or find open questions

Devise an experimental plan including suitable methods, controls, and timing

Publication grade write up and conference level presentation of new data

Format Seminar (3 SWS), practical work (37 SWS)

Duration 6 months

when? 4th semester

prerequisite 3 modules, 4 lab projects

Evaluation Oral presentation of results (not graded)

Written thesis (Þ graded by supervisor and if necessary a 2nd

referee)

Responsible Head of the examination committee

organizers IFIB group leaders, module organizers, other labs after confirmation

Credit points 30 CP

Final Grade

As you progress from undergraduate studies via the master with us to a doctorate or

employment outside academia, grades become less important and experimental skills,

experience, contacts, and publications gain in weight. Nevertheless, the final grade of the

Masters in Biochemistry will be of some influence.

The final grade is composed in equal part of the grades of the Advanced Biochemistry

lecture series, your 3 best modules, and the master thesis. If you completed 4 modules, the

best grades will be used automatically. It will thus be based in equal parts on the oral

examination after the lectures, the mean grade of your modules, and the overall grade of

your master thesis.

Links

We will use the ILIAS platform (https://ovidius.uni-tuebingen.de/ilias3/) as a principle way of

organizing the courses and we hope that you will use your editing rights there to exchange

information between each other and with us. There, you will find all elements of the current

semester represented as ILIAS objects. In addition, there is a collection of frequently asked

questions, useful links, and areas with content jointly generated by students and faculty.

Remember to regularly check our calendar for course changes and additional events:

http://tinyurl.com/mbioch-cal.

Wondering where things are? Check the map: http://tinyurl.com/mbioch-map.

Preparation

If your bachelor was in a related discipline or if you just want to brush up a little to be able to

start at full speed, we recommend the following books: Alberts, Molecular Biology of the Cell, 2014, http://amzn.to/1K22W7r, Berg,.. Stryer, Biochemistry, 2015,

http://amzn.to/1ExNQAt.

Also, we would recommend to read current research articles. The following journals are

usually a good choice: eLife, PLoS Biology, Nature, Science, or Cell.

To tune into the spoken scientific language, browse the following site for scientific talks: TED

(not all biochemistry, http://tinyurl.com/n3yndqv), Nobel talks (nobelprize.org/mediaplayer/),

HS talks (only the first minutes free, http://tinyurl.com/m2uh8ds).

And/or consider taking an online course on edX.org or Coursera.org.

master guide v10 unpublished - daad

Documents